Bacterial genetics and genomics:
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Bosa Raton
CRC Press
[2020]
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| Beschreibung: | xxiv, 389 Seiten Illustrationen, Diagramme |
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| 245 | 1 | 0 | |a Bacterial genetics and genomics |c Lori. A. S. Snyder |
| 264 | 1 | |a Bosa Raton |b CRC Press |c [2020] | |
| 300 | |a xxiv, 389 Seiten |b Illustrationen, Diagramme | ||
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| adam_text | Contents
Note to Reader
Acknowledgments
About the Author
Welcome to the World of Bacterial
Genetics and Genomics
Further reading
Part I DNA, Genes, and Genomes
Chapter 1
DNA
Life originated from RNA with DNA
evolving later
Nucleic acids are made of nucleoside
bases attached to a phosphate
sugar backbone
DNA was discovered in 1869 and
identified as the genetic material
75 years later
The first X-ray images of DNA were
taken in 1937 with the structure
finally solved in 1953
DNA consists of two bidirectional strands
joined by deoxyribose
sugars and nucleotide bases
DNA is copied semi-conservatively
every time a cell divides
Replication starts at the origin of replication
and requires primers
DNA polymerase can only add
bases in the S to 3 direction
Bacterial DNA can occur in several
different forms 17
The replication of plasmids is
independent of the replication of
the chromosome(s) 18
Key points 18
Terms, questions, and discussions 19
Key terms 19
Self-study questions 20
Discussion topics 20
Further reading 20
Chapter 2
Genes 23
Genes are features in the DNA that encode
proteins 23
Bacterial transcription generates
RNA based on the DNA sequence 24
Initiation of transcription 24
Transcriptional elongation 25
Transcriptional termination 26
Bacterial translation produces
proteins based on the mRNA
sequence 27
Ribosomes 27
Translation initiation 28
Translational elongation 28
Translational termination and
ribosome recycling 29
Coupled transcription-translation
in bacteria has mRNA being made and
used to produce proteins in tandem 29
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Contents
Bacteria can have more than one
gene on an mRNA strand and form operons 30
Open reading frames are regions of the
ONA between termination codons 31
When a CDS is a gene 32
Expression of genes is controlled -
not all genes are on all of the time 34
Sigma factors are responsible
for RNA polymerase promoter recognition 35
Regulatory proteins change the
level of transcription 36
Repressor proteins prevent or
reduce the transcription of genes 36
Activator proteins contribute to
the expression or increased
expression of genes 37
Regulatory RNAs may have an impact upon
transcription 37
Riboswitches alter the transcript
that includes their sequence 38
Global regulators control the transcription
of multiple genes 38
Essential genes and accessory genes 39
Key points 40
Terms, questions, and discussions 42
Key terms 42
Self-study questions 43
Discussion topics 43
Further reading 43
Chapter 3
Genomes 45
Bacterial chromosomes carry the genetic
material of the organism 45
Some bacteria have multiple chromosomes 46
Plasmids contribute additional
genetic features 46
When DNA that looks like a plasmid
may actually be a chromosome 47
Prophages add bacteriophage
genomes to a bacterial genome 47
The sizes of bacterial genomes are
characteristic of bacterial species 48
Contributions of the core genome
to defining the species and the
accessory genome to defining
the strain 48
Bacterial genomes are densely packed 49
DNA base composition differs
between species 49
Base composition differs between
coding region 50
The origin of replication impacts the base
composition 50
Genomic architecture can impact
gene expression 52
Conservation of the order of genetic features
between bacterial species 52
Supercoiling can also influence gene
expression 53
Distribution of noncoding genetic
features in the bacterial chromosome 54
Mutations in the bacterial genome 55
Translocations can change the order
of genetic features in a genome 56
Inversions flip the DNA strand upon which
genetic features are located 57
Recombination changes the genome 57
Horizontal gene transfer introduces
new genetic material 57
Transformation involves bacterial uptake
of DNA from its surroundings 58
Conjugation is an encoded mechanism
for DNA transfer from one bacterial cell to
another 59
The process of transduction can
introduce bacteriophage DNA into a
bacterial cell 60
Key points 60
Terms, questions, and discussions ^
Key terms 61
Self-study questions 61
Discussion topics 62
Further reading 62
Contents ix
Part II RNA, Transcriptional
Regulation, and Transcriptomes
Chapter 4
RNA
Bacterial mRN As are translated into
proteins as they are being transcribed
The size of mRNA is determined by the
genes it encodes
The start of the S end of mRNA is
dictated by its promoter region
Not all transcripts are translated into
proteins
There are untranslated regions at
the S end of the mRNA transcript
Features at the 3 end of the mRNA
transcript can influence the
expression of encoded genes
Stability of RNA and its degradation by
nucleases and hydrolysis
Secondary structures formed by mRNAs
impact ribosome binding and translation
initiation
Secondary structures formed by mRNA
influence translational termination
Tertiary structures within mRNAs impact
expression of the encoded gene
RNA thermometers modify the expression of
proteins from mRNA based on temperature
Polyadenylation of mRNA is not just for
eukaryotes
Bacterial tRNAs are folded into tight
structures
tRNA transcripts undergo post-
transcriptional processing
rRNAs are essential components of the
ribosome
The bacterial cell also contains noncoding
RN As that can regulate other RNAs
Key points
Terms, questions, and discussions
Key terms
Self-study questions
Discussion topics
Further reading
Chapter 5
Transcriptional Regulation 81
Regulation of gene expression at the
level of transcription 81
The classic example of transcriptional
regulation: The lac operon 82
The lac operon is also subject to catabolite
repression 83
The actions of the corepressor tryptophan
on the trp operon 84
An attenuation mechanism controls
the expression of the trp operon 85
Genes are regulated locally by frans-acting
factors 87
Repressors, activators, and inducers can
influence the expression of many genes 87
Two-component regulators sense change
and alter transcription 88
DNA changes in the promoter region locally
regulate transcription in cis 89
Programmed changes to DNA can
alter transcription locally 89
Sigma factors are essential for the
initiation of gene transcription 91
Sigma factors can orchestrate global
regulation of gene transcription 92
Control of sigma factor activity involves
several components 92
Global regulation can be influenced
by the binding of chromatin proteins
to the DNA 93
The H-NS protein binds to DNA,
making regions unavailable for transcription 93
HU and IHF are homologous proteins that
act in a similar way upon DNA 94
The Fis nucleoid protein is involved in
the regulation of rRNA transcription 94
Quorum sensing causes transcriptional
changes within the bacterial cell 94
Biofilm formation is a specialized response
to quorum sensing and other signals 95
Cyclic di-GMP is involved in the regulation
of a range of functions within the
bacterial cell 95
The small molecule ppGpp is an
indicator of the state of the bacterial cell 95
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Protein thermosensors regulate expression
of proteins via transcriptional regulation
Stability and degradation of mRNA by
ribonudease III impacts upon whether a
transcript is expressed as a protein
Regulation of gene expression can be
through the action of RNA binding proteins 96
Key points 97
Terms, questions, and discussions 97
Key terms 97
Self-study questions 98
Discussion topics 98
Further reading 98
Chapter 6
Transcriptomes 101
The transcriptome changes over time 101
The transcriptome changes due to changing
conditions 102
Expression of genes outside the lac operon
in response to glucose and lactose 103
Tryptophan and its impact on the
transcriptome 104
Transcriptomic changes occur when
bacterial cells contact host cells 105
Changes in temperature can trigger
changes in the transcriptome 106
Expression of key proteins can indicate a
response to temperature change 106
Different types of thermosensors can
alter gene expression due to temperature 107
Global gene regulation can occur in
response to iron 108
Bacterial cells require nutrients and
regulate gene expression to get what they
need 109
Each bacterial cell in a culture is different 109
Expression profiling provides a population
level understanding of regulation 110
The expression of multiple genes is
coordinated together across the
chromosome 111
The transcriptional network landscape
can have topology 111
Key points 112
Terms, questions, and discussions nj
Key terms 112
Self-study questions 112
Discussion topics 113
Further reading 113
Part III Proteins, Structures, and
Proteomes
Chapter 7
Proteins 117
Amino acids contain an amine group,
a carboxyl group, and a side chain 117
The production of functional proteins
from amino acids 117
The inflexible nature of the peptide bond
imposes limits on the amino acids 118
Amino acids are generally present as
zwitterions 118
There are 20 amino acids encoded in
the standard genetic code of DNA 119
The codons present in the DNA sequence is
species specific 119
The amino acids that can be made by
bacteria are species specific 120
Most amino acids are l stereoisomer
a-amino acids 120
The classification of an amino acid is
determined by its side chain 120
Glycine is small and flexible 121
Alanine is abundant and versatile 121
Arginine has a positively charged
side chain 121
Asparagine was the first amino acid
identified 121
Aspartic acid is negatively charged
and binds to positively charged molecules 122
Cysteine forms disulfide bonds with other
cysteines 122
Glutamic acid is a large, acidic
amino acid 122
Glutamine has an uncharged side chain 123
Contents xi
Histidine has a large positively charged side chain containing a ring structure 123 Quaternary amino acid structures form when tertiary structures come
Isoleucine has a branched side chain 123 together 131
Leucine is similar to isoleucine, although its branched side chain is Proteins are assisted in folding by chaperones 132
configured differently 123 Some proteins include more than just
Lysine has a long, flexible side chain 123 amino acids 133
Methionine is at the start of all translation 124 Phosphorylation adds a phosphate group
Phenylalanine has a rigid ring to a protein, often activating the protein 133
structure side chain 124 Lipids are added to proteins
The side chain for proline loops post-translationally, adding a hydrophobic region 133
back to the amine group Serine has an uncharged side chain 124 Glycoproteins have a sugar added to the protein 134
that readily donates hydrogen 125 Some proteins are modified through
Threonine is similar to serine with an the addition of an oxygen 134
uncharged polar side chain Tryptophan has a large side chain 125 Acetylation adds an acetyl group to a peptide chain 134
with a double ring structure Tyrosine has a hydrophobic ring structure side chain 125 125 Succinylation and acetylation can happen at the same amino acid, but not both at the same time 135
Valine has a branched hydrophobic side chain, similar to isoleucine and leucine 125 Methylation post-translationally adds a methyl group to a protein 136
Bacterial proteins can include other amino acids beyond the 20 with 125 126 Nitrosylation of bacterial proteins can modify regulatory networks 136
codons Key points Modification can remove the fMet at the start of the peptide chain 136
Terms, questions, and discussions 126 Proteins are made in the bacterial cytoplasm
Key terms 126 but may be transported elsewhere 137
Self-study questions 127 Secreted proteins carry a signal
Discussion topics 127 to aid in their transport out of the cell 138
Further reading 127 Key points 139
Chapter 8 Terms, questions, and discussions Key terms 139 139
Protein Folding and Self-study questions 140
Structure 129 Discussion topics 140
Primary amino acid structure is the linear sequence of amino acids joined by peptide bonds 129 Further reading Chapter 9 141
Secondary amino acid structure is a folding of the primary sequence of 129 131 Multiprotein Systems and Proteomes 143
amino acids Tertiary amino acid structures form when secondary structures come together Some cellular structural components are not directly encoded by genes 143
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Contents
Genetics of lipopolysaccharide production
The LPS has to be assembled and
translocated to the outer surface
of the cell
Peptidoglycan is built by proteins encoded
in a cluster of genes
Bacterial membrane phospholipids
are made by proteins
Extracellular polysaccharides make up
the bacterial capsule
Proteins make up bacterial cell structures
Some bacterial proteins are enzymes that
actively cause change
Bacterial secretion systems move
proteins across the bacterial membranes
The Type 1 Secretion System takes proteins
across both membranes in one step
Type 2 Secretion Systems take a protein from
the periplasm out of the cell
The Type 3 Secretion System can
inject proteins like a syringe
The Type 4 Secretion System includes
conjugation systems and DNA uptake
systems
Type 5 Secretion Systems are proteins that
secrete themselves
Type 6 Secretion Systems transport proteins
into other cells, including other bacteria
Gram-positive secretion systems
can aid protein transport across the thick
peptidoglycan layer
Efflux pump systems transport harmful
substances out of the bacterial cell
All of the expressed proteins are the
proteome
Mass spectrometry technology enables
the study of proteomes
Proteomics aids in identification of the
core genome
Mass spectrometry is being used
diagnostically to identify bacteria
Proteomics can be used to investigate
antibiotic resistance
Key points
Terms, questions, and discussions
Key terms
Self-study questions 159
Discussion topics 159
Further reading 159
Part IV Genetics, Genomics,
and Bioinformatics
Chapter 10
Genetics 163
Terms and conventions in the field
of bacterial genetics are straightforward 163
Humans have understood about
traits and inheritance long before
the term genetics 164
DNA was ignored and believed to
be too simple to be the genetic
material of inheritance 164
Bacterial genetics was the key to
demonstrating the importance of DNA 165
Insights following the recognition
of DNA as the genetic material led
us to where we are today 165
Bacterial genetics is the cornerstone
of ail genetics 166
The identification and isolation of
restriction enzymes is important for
genetics research 166
There are four types of restriction
enzymes, with type 2 being used most
in laboratories 167
The genetics of bacteria was
unraveled using conjugation 168
Physical maps can be made for any
bacterial species using restriction enzymes 169
Experimentation reveals whether a CDS is a
gene and what its function may be 170
Library generation and library screening
can identify genes and their functions 170
Random mutagenesis identifies genes
that have non-essential functions 171
The functions of genes can be determined
using knockout technologies 171
Knockout a gene and complement it back to
check the phenotype is caused by the
knocked out gene 172
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Bacterial research has helped shape the
field of genetics
Key points
Terms, questions, and discussions
Key terms
Self-study questions
Discussion topics
Further reading
Chapter 11
Genomics
Automation of Sanger sequencing
launched the era of bacterial
genome sequencing
The first genome sequence of a
free-living organism was bacterial
Early genome sequencing of bacteria
provided opportunities for new
insight and innovation
Bacterial genome sequencing
required and fueled innovation
The emergence of next-generation
sequencing technologies greatly
increased sequence data
Next-generation sequencing has limitations
Bacterial genome-sequencing
projects shift focus due to next-generation
sequencing limitations
Next-generation sequencing enables a
massive expansion of comparative genomics
Next-generation sequencing and
epidemiology
Bacterial genome-sequencing identification
of the source of outbreaks
Quick, easy sequencing means bacterial
genomes can be given a second look
Bacterial genome sequencing can uncover
bacteria never before studied
Single-molecule sequencing is more
sensitive and produces longer read lengths
Two single-molecule sequencing
technologies have emerged, including
physical reading of the DNA
Key points 186
Terms, questions, and discussions 187
Key terms 187
Self-study questions 187
Discussion topics 188
Further reading 188
Chapter 12
Bioinformatics 189
A lot can be learned from looking at strings
of A s, T s, G s, and C s 189
Bioinformatics is essential for interpreting
sequence data 189
Annotation predicts features in sequence
data and notes their locations 191
The process of creating an annotation
starts with the DNA sequence data 192
Multiple lines of investigation into
the sequence data features support
the annotation 193
Annotations tend to start with
potential genes 193
Homology and conserved protein
domains can help identify the
potential function of a CDS 194
Automated annotations rapidly produce
an annotation that needs manual curation 195
Some features in sequence data and
annotation data can confuse new
annotations 195
Naming genes is not straightforward,
with some genes having more than
one name 196
Annotation errors, including spelling
mistakes, can spread from one annotation
to many others 196
Gene locus identifiers are handy
for labeling features in annotations,
but reveal nothing about function 196
There are three major public
databases for sequence data 197
Comparative genomics finds that
there are commonly shared genes
and unique genes 197
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Comparative genomics can be done
without assembly or annotation of
sequencing data 199
Horizontally transferred gene sequences
tend to carry a signature that can identify
them 200
Genome sequence analysis can find
unexpected features in the sequence data 201
Comparative genomics on closely
related strains can reveal
biologically important information 201
Comparative genomics between
non-related species gives insight into
bacterial evolution 20B
Strain identification using sequencing
data is a powerful tool for tracking
bacterial transmission 203
Function predictions can be made
based on sequence similarity 204
Key points 206
Terms, questions, and discussions 206
Key terms 206
Self-study questions 206
Discussion topics 207
Further reading 207
PartV Bacterial Response,
Adaptation, and Evolution
Chapter 13
Bacterial Response 211
Studying responses often happens in pure
bacterial cultures 212
Two-component regulatory systems enable
bacteria to respond to their environment 212
Bacteria decrease host glucose levels
to impair the host immune response 213
Bacteria modulate the immune response
using the Type 3 Secretion System 213
Some bacteria cheat and let others
do all the work with their Type 3 Secretion
Systems 214
A response might only be appropriate
when the population is large 215
Quorum sensing makes a beautiful
bioluminescent glow in the ocean
and in the lab 216
Quorum sensing is a process to
tally the bacterial cells 216
Biofilms mature due to quorum
sensing signals 217
Quorum sensing has cheaters 218
Going from free living to biofilm involves
changes in gene expression 218
Biofilm dispersal is regulated by
different elements between different
bacterial species 219
c-di-GMP plays a key role in biofilm
regulation in P aeruginosa 220
Bacteria have their own immune system
to protect them from bacteriophages 221
Key points 222
Terms, questions, and discussions 223
Key terms 223
Self-study questions 223
Discussion topics 224
Further reading 224
Chapter 14
Bacterial Adaptation 227
Within a niche, bacteria have to adapt to
their peers and other bacteria 227
GIcNAc has a role as a signaling molecule
as well as being part of the bacterial
cell wall 228
Competitor bacteria can be killed with
specialized Type 6 Secretion Systems 228
Caulobacter differentiate between motile
and sessile cells 229
Staphylococcus aureus secrete several
proteins to inhibit host defenses as part of
adapting their niche to their needs 230
Intracellular bacteria adapt to life inside
the cells of the host 231
Mycobacterium tuberculosis adapts
both itself and its host 232
Legionella adapt by knowing when
not to grow 232
Contents xv
Group A Streptococci within the host
experience adaptation, mutation, and death 233
Adaptation of the host to enhance spread
of the infection 234
Listeria monocytogenes can adapt
to an intracellular or soil niche 234
Environmental bacteria like Lactobacillus
plantarum can live in a wide variety of niches 234
Pseudomonas aeruginosa adapts to
live in a wide variety of environments 235
Mastitis-causing bacteria Streptococcus uberis
can adapt to different niches within cows 235
Bacteria adapt to avoid recognition by the
host immune system through antigenic
variation 236
Several different species use gene conversion
as a mechanism of antigenic variation 236
Phase variation is an important means of
adaptation, but is not a means of response 237
Small noncoding RNAs also have
a role in enabling bacteria to adapt 238
Key points 238
Terms, questions, and discussions 239
Key terms 239
Self-study questions 239
Discussion topics 239
Further reading 240
Chapter 15
Bacterial Evolution 241
Evolution can be studied within bacterial
cultures 241
Bacteria can evolve within the
host and we can see this happen with
sequencing technologies 242
Antibiotic resistance is an easily observable
evolutionary event 244
Mutations can be introduced into bacterial
DNA by a variety of factors 244
Yersinia pestis, causing plague, has evolved
from Yersinia pseudotuberculosis 245
Neisseria meningitidis, causing
meningococcal meningitis and septicemia,
acquired its capsule fairly recently 246
The number of pseudogenes in a
species can reveal how recently it has
adapted to a new niche 247
Evolution of the bacterial surface to cope
with the immune system and vaccines 247
Horizontal gene transfer can bring new
genes into a species, contributing to its
evolution 248
The particular nature of an environmental
niche can create opportunities for evolution 249
It is possible for completely new genes to
evolve 249
Key points 250
Terms, questions, and discussions 250
Key terms 250
Self-study questions 251
Discussion topics 251
Further reading 251
Part VI Gene Analysis, Genome
Analysis, and Laboratory
Techniques
Chapter 16
Gene Analysis Techniques 255
Sequence searches are done to find
out what else is similar to this gene 255
Before there was BLAST, there was FASTA 255
BLAST quickly finds the most similar
sequences 256
There are five basic versions of BLAST,
addressing different search tasks 258
There are other versions of BLAST
that do specialist searches 259
Searches can look for more than
just similarities 260
Alignments of similar sequences are useful
for further analysis 261
Local alignments to compare the portions
of the sequence that are similar 261
Global alignments will align any sequences,
similar or not 262
More complex comparisons need
multiple sequence alignment algorithms 263
XVI
Contents
Protein localization can be predicted from
the amino acids 265
DNA sequence to gene to amino acid
sequence to 3D protein structure, ideally 267
De novo protein structure predictions base
structures just on the amino acids 267
Transmembrane helix prediction can find
membrane proteins 267
Homology modeling of proteins
bases structures on known structures 267
Protein threading can suggest a
protein structure based on
protein fold similarity 268
Some gene tools are used to help
design laboratory experiments 268
Key points 270
Terms, questions, and discussions 270
Key terms 270
Self-study questions 270
Discussion topics 271
Further reading 272
Chapter 17
Genome Analysis
Techniques 273
A few things happen to the genome
sequencing data before the search
for genes 273
Identification of features in genomic data
is a key aspect of analysis 274
Automated annotation pipelines usefully
combine feature identification tools 275
Visualization of an automatically generated
annotation can aid manual curation 277
Comparisons show orthologues and
paralogues, revealing evolutionary
relationships between genes 279
Genomes can be aligned, just like
genes can be aligned 279
Mauve genome alignments make stunning
figures, as well as being a useful research
tool 280
There is value in typing data, even
in the genomics age 283
Galaxy provides a full analysis
suite for biological data 284
Key points 286
Terms, questions, and discussions 286
Key terms 286
Self-study questions 286
Discussion topics 287
Further reading 287
Chapter 18
Laboratory Techniques 289
The study of bacterial genetics and genomics
fundamentally focuses on DNA, therefore
starting with lysis of bacterial cells for DNA
extraction 289
DNA extraction using phenol produces very
pure, large quantities of DNA 290
Phase separation and DNA precipitation
in a phenol DNA extraction result in
isolated DNA 290
Additional considerations for phenol
DNA extraction can improve the outcome 292
Most DNA extractions use columns 292
Troubleshooting DNA extractions
can increase yield and quality of
the DNA 293
A quick (and dirty) DNA extraction
can be achieved by boiling 294
The first recombinant DNA
experiments in the 1970s were made
possible because of restriction
enzymes, which are still used today 294
Set up a restriction digestion with
the optimal reaction conditions 295
There are a few additional considerations to
remember when doing restriction digestions 296
Restriction digestions are used to change
DNA sequences and join sequences together 296
Cut ends of DNA need to be ligated
together to complete cloning 297
Important considerations when performing
ligations 298
Cloning of sequences is often
important in bacterial genetics and
genomics research 298
Contents xvii
TA cloning exploits a feature of PCR to
rapidly clone sequences
Some commercially available kits augment
ligation and cloning with accessory proteins
and exploitation of other systems
Antibiotic resistance markers on plasmids
help us find the transformed bacterial
colonies
Blue-white screening helps us find the
colonies transformed with plasmids with
the insert
Laboratory techniques of molecular
biology are able to copy segments of DNA
in processes similar to replication
PCR can be altered slightly to address
experimental needs
Site-directed mutagenesis systems help
researchers make specific changes to DNA
Loop-mediated isothermal
amplification (LAMP) quickly amplifies
DNA at a single temperature
Following in vitro manipulation of DNA,
it has to be transformed into a bacterial cell
Calcium chloride provides a quick method to
obtain competent cells for immediate use
Chemically competent cells with Inoue
buffer have the best reputation for good
rates of transformation and reliability
Chemically competent cells can be made
with TSS buffer
Transformations using chemically
competent cells use similar methods,
regardless of how the cells were made
Electroporation provides an alternative
to chemically competent cells
The process of electroporation is sensitive to
salts, but quick to perform
Expression studies rely on extraction of
high-quality RNA, which means controlling
RNases
RNA extraction columns work similarly
to DNA extraction columns, with some
slight variations
Acidic phenol extraction of RNA makes
high-quality, pure RNA
Key points
300 Terms, questions, and discussions 315
Key terms 315
Self-study questions 315
300 Discussion topics 316
Further reading 317
302 Part VII Applications of Bacterial Genetics and Genomics
302 Chapter 19
303 Biotechnology 321
Biotechnology is far older than genetic
304 engineering Biotechnology impacts many aspects of 321
305 our lives and of research 322
Large quantities of bacteria are grown in bioreactors to yield large quantities of
307 recombinant proteins Human insulin expressed in Escherichia 322
307 coli is a classic example of biotechnology Many recombinant drugs have been made 323
309 since insulin 324
Recombinant production of influenza virus vaccines 324
309 Live recombinant vaccines use live bacteria to deliver antigens 325
310 Bioremediation uses the microbial world to correct the pollutants we have introduced into the natural world 325
311 Bioremediation using bacteria present in the environment can help us reclaim sites 326
312 Genetic modification for bioremediation can provide
312 organisms with new features 327
Bacteria can be a renewable source of bioenergy 327
312 Key points 328
Terms, questions, and discussions 329
313 Key terms 329
Self-study questions 329
313 Discussion topics 330
315 Further reading 330
Contents
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Chapter 20
Infectious Diseases
331
The study of bacterial pathogen
genes has led to new drugs to
control infectious diseases
Genomics can aid in the search
for new antibiotics
Some old drugs are getting a new lease
of life due to greater depth of
understanding
Bacterial genomics has led to the
development of new vaccines
Reverse vaccinology is providing
leads for several bacterial diseases
New drugs are being developed
that will contain the virulence of bacteria
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Monoclonal antibody therapy is useful for a
variety of human diseases, including
infectious diseases 336
Sequencing changes our understanding of
the virulence factors that are important 337
Gene sequencing and genome
sequencing improves the resolution of
epidemiology of bacterial infectious diseases 337
Genome sequencing can improve infection
control for surgical site infections
Horizontal gene transfer between
pathogens revealed by sequencing shows
worrying trends in evolution
Genome sequencing is improving our
understanding of infections that
could impact transplant recovery
Putting discoveries into practice
Key points
Terms, questions, and discussions
Key terms
Self-study questions
Discussion topics
Further reading
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Chapter 21
Bacteriophages
Bacteriophages have been studied
for just over 100 years
Bacteriophages cannot replicate without
bacterial cells 344
Some bacteriophages enter latency
for a period before replication 345
The NIS2 bacteriophage has a very
small genome and was the first
genome sequenced 346
Important discoveries about genetics have
been made by studying bacteriophage X 347
TheT4 bacteriophage has a characteristic
morphology 348
The ipXl 74 bacteriophage was the
first DNA genome sequenced 349
Transduction is an important
source of horizontal gene
transfer for bacteria 349
Bacteriophages also contribute to
bacterial evolution through chromosomal
rearrangements 350
Bacteriophage and prophage genome
evolution can provide interesting insights 350
Bacteria have evolved strategies to avoid
bacteriophage infection 351
Even if bacteria become infected by
bacteriophage nucleic acids, they
can still fight back 351
Bacteriophage resistance that fights
back and uses the bacteriophages
for its own ends 352
Bacteriophage therapy is a potential
alternative treatment for
antimicrobial resistant bacteria 353
Key points 354
Terms, questions, and discussions 354
Key terms 354
Self-study questions 355
Discussion topics 355
Further reading 355
Glossary 357
Glossary of Bacterial Species 371
|
| adam_txt |
Contents
Note to Reader
Acknowledgments
About the Author
Welcome to the World of Bacterial
Genetics and Genomics
Further reading
Part I DNA, Genes, and Genomes
Chapter 1
DNA
Life originated from RNA with DNA
evolving later
Nucleic acids are made of nucleoside
bases attached to a phosphate
sugar backbone
DNA was discovered in 1869 and
identified as the genetic material
75 years later
The first X-ray images of DNA were
taken in 1937 with the structure
finally solved in 1953
DNA consists of two bidirectional strands
joined by deoxyribose
sugars and nucleotide bases
DNA is copied semi-conservatively
every time a cell divides
Replication starts at the origin of replication
and requires primers
DNA polymerase can only add
bases in the S' to 3' direction
Bacterial DNA can occur in several
different forms 17
The replication of plasmids is
independent of the replication of
the chromosome(s) 18
Key points 18
Terms, questions, and discussions 19
Key terms 19
Self-study questions 20
Discussion topics 20
Further reading 20
Chapter 2
Genes 23
Genes are features in the DNA that encode
proteins 23
Bacterial transcription generates
RNA based on the DNA sequence 24
Initiation of transcription 24
Transcriptional elongation 25
Transcriptional termination 26
Bacterial translation produces
proteins based on the mRNA
sequence 27
Ribosomes 27
Translation initiation 28
Translational elongation 28
Translational termination and
ribosome recycling 29
Coupled transcription-translation
in bacteria has mRNA being made and
used to produce proteins in tandem 29
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Bacteria can have more than one
gene on an mRNA strand and form operons 30
Open reading frames are regions of the
ONA between termination codons 31
When a CDS is a gene 32
Expression of genes is controlled -
not all genes are on all of the time 34
Sigma factors are responsible
for RNA polymerase promoter recognition 35
Regulatory proteins change the
level of transcription 36
Repressor proteins prevent or
reduce the transcription of genes 36
Activator proteins contribute to
the expression or increased
expression of genes 37
Regulatory RNAs may have an impact upon
transcription 37
Riboswitches alter the transcript
that includes their sequence 38
Global regulators control the transcription
of multiple genes 38
Essential genes and accessory genes 39
Key points 40
Terms, questions, and discussions 42
Key terms 42
Self-study questions 43
Discussion topics 43
Further reading 43
Chapter 3
Genomes 45
Bacterial chromosomes carry the genetic
material of the organism 45
Some bacteria have multiple chromosomes 46
Plasmids contribute additional
genetic features 46
When DNA that looks like a plasmid
may actually be a chromosome 47
Prophages add bacteriophage
genomes to a bacterial genome 47
The sizes of bacterial genomes are
characteristic of bacterial species 48
Contributions of the core genome
to defining the species and the
accessory genome to defining
the strain 48
Bacterial genomes are densely packed 49
DNA base composition differs
between species 49
Base composition differs between
coding region 50
The origin of replication impacts the base
composition 50
Genomic architecture can impact
gene expression 52
Conservation of the order of genetic features
between bacterial species 52
Supercoiling can also influence gene
expression 53
Distribution of noncoding genetic
features in the bacterial chromosome 54
Mutations in the bacterial genome 55
Translocations can change the order
of genetic features in a genome 56
Inversions flip the DNA strand upon which
genetic features are located 57
Recombination changes the genome 57
Horizontal gene transfer introduces
new genetic material 57
Transformation involves bacterial uptake
of DNA from its surroundings 58
Conjugation is an encoded mechanism
for DNA transfer from one bacterial cell to
another 59
The process of transduction can
introduce bacteriophage DNA into a
bacterial cell 60
Key points 60
Terms, questions, and discussions ^
Key terms 61
Self-study questions 61
Discussion topics 62
Further reading 62
Contents ix
Part II RNA, Transcriptional
Regulation, and Transcriptomes
Chapter 4
RNA
Bacterial mRN As are translated into
proteins as they are being transcribed
The size of mRNA is determined by the
genes it encodes
The start of the S' end of mRNA is
dictated by its promoter region
Not all transcripts are translated into
proteins
There are untranslated regions at
the S' end of the mRNA transcript
Features at the 3' end of the mRNA
transcript can influence the
expression of encoded genes
Stability of RNA and its degradation by
nucleases and hydrolysis
Secondary structures formed by mRNAs
impact ribosome binding and translation
initiation
Secondary structures formed by mRNA
influence translational termination
Tertiary structures within mRNAs impact
expression of the encoded gene
RNA thermometers modify the expression of
proteins from mRNA based on temperature
Polyadenylation of mRNA is not just for
eukaryotes
Bacterial tRNAs are folded into tight
structures
tRNA transcripts undergo post-
transcriptional processing
rRNAs are essential components of the
ribosome
The bacterial cell also contains noncoding
RN As that can regulate other RNAs
Key points
Terms, questions, and discussions
Key terms
Self-study questions
Discussion topics
Further reading
Chapter 5
Transcriptional Regulation 81
Regulation of gene expression at the
level of transcription 81
The classic example of transcriptional
regulation: The lac operon 82
The lac operon is also subject to catabolite
repression 83
The actions of the corepressor tryptophan
on the trp operon 84
An attenuation mechanism controls
the expression of the trp operon 85
Genes are regulated locally by frans-acting
factors 87
Repressors, activators, and inducers can
influence the expression of many genes 87
Two-component regulators sense change
and alter transcription 88
DNA changes in the promoter region locally
regulate transcription in cis 89
Programmed changes to DNA can
alter transcription locally 89
Sigma factors are essential for the
initiation of gene transcription 91
Sigma factors can orchestrate global
regulation of gene transcription 92
Control of sigma factor activity involves
several components 92
Global regulation can be influenced
by the binding of chromatin proteins
to the DNA 93
The H-NS protein binds to DNA,
making regions unavailable for transcription 93
HU and IHF are homologous proteins that
act in a similar way upon DNA 94
The Fis nucleoid protein is involved in
the regulation of rRNA transcription 94
Quorum sensing causes transcriptional
changes within the bacterial cell 94
Biofilm formation is a specialized response
to quorum sensing and other signals 95
Cyclic di-GMP is involved in the regulation
of a range of functions within the
bacterial cell 95
The small molecule ppGpp is an
indicator of the state of the bacterial cell 95
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Protein thermosensors regulate expression
of proteins via transcriptional regulation
Stability and degradation of mRNA by
ribonudease III impacts upon whether a
transcript is expressed as a protein
Regulation of gene expression can be
through the action of RNA binding proteins 96
Key points 97
Terms, questions, and discussions 97
Key terms 97
Self-study questions 98
Discussion topics 98
Further reading 98
Chapter 6
Transcriptomes 101
The transcriptome changes over time 101
The transcriptome changes due to changing
conditions 102
Expression of genes outside the lac operon
in response to glucose and lactose 103
Tryptophan and its impact on the
transcriptome 104
Transcriptomic changes occur when
bacterial cells contact host cells 105
Changes in temperature can trigger
changes in the transcriptome 106
Expression of key proteins can indicate a
response to temperature change 106
Different types of thermosensors can
alter gene expression due to temperature 107
Global gene regulation can occur in
response to iron 108
Bacterial cells require nutrients and
regulate gene expression to get what they
need 109
Each bacterial cell in a culture is different 109
Expression profiling provides a population
level understanding of regulation 110
The expression of multiple genes is
coordinated together across the
chromosome 111
The transcriptional network landscape
can have topology 111
Key points 112
Terms, questions, and discussions nj
Key terms 112
Self-study questions 112
Discussion topics 113
Further reading 113
Part III Proteins, Structures, and
Proteomes
Chapter 7
Proteins 117
Amino acids contain an amine group,
a carboxyl group, and a side chain 117
The production of functional proteins
from amino acids 117
The inflexible nature of the peptide bond
imposes limits on the amino acids 118
Amino acids are generally present as
zwitterions 118
There are 20 amino acids encoded in
the standard genetic code of DNA 119
The codons present in the DNA sequence is
species specific 119
The amino acids that can be made by
bacteria are species specific 120
Most amino acids are l stereoisomer
a-amino acids 120
The classification of an amino acid is
determined by its side chain 120
Glycine is small and flexible 121
Alanine is abundant and versatile 121
Arginine has a positively charged
side chain 121
Asparagine was the first amino acid
identified 121
Aspartic acid is negatively charged
and binds to positively charged molecules 122
Cysteine forms disulfide bonds with other
cysteines 122
Glutamic acid is a large, acidic
amino acid 122
Glutamine has an uncharged side chain 123
Contents xi
Histidine has a large positively charged side chain containing a ring structure 123 Quaternary amino acid structures form when tertiary structures come
Isoleucine has a branched side chain 123 together 131
Leucine is similar to isoleucine, although its branched side chain is Proteins are assisted in folding by chaperones 132
configured differently 123 Some proteins include more than just
Lysine has a long, flexible side chain 123 amino acids 133
Methionine is at the start of all translation 124 Phosphorylation adds a phosphate group
Phenylalanine has a rigid ring to a protein, often activating the protein 133
structure side chain 124 Lipids are added to proteins
The side chain for proline loops post-translationally, adding a hydrophobic region 133
back to the amine group Serine has an uncharged side chain 124 Glycoproteins have a sugar added to the protein 134
that readily donates hydrogen 125 Some proteins are modified through
Threonine is similar to serine with an the addition of an oxygen 134
uncharged polar side chain Tryptophan has a large side chain 125 Acetylation adds an acetyl group to a peptide chain 134
with a double ring structure Tyrosine has a hydrophobic ring structure side chain 125 125 Succinylation and acetylation can happen at the same amino acid, but not both at the same time 135
Valine has a branched hydrophobic side chain, similar to isoleucine and leucine 125 Methylation post-translationally adds a methyl group to a protein 136
Bacterial proteins can include other amino acids beyond the 20 with 125 126 Nitrosylation of bacterial proteins can modify regulatory networks 136
codons Key points Modification can remove the fMet at the start of the peptide chain 136
Terms, questions, and discussions 126 Proteins are made in the bacterial cytoplasm
Key terms 126 but may be transported elsewhere 137
Self-study questions 127 Secreted proteins carry a signal
Discussion topics 127 to aid in their transport out of the cell 138
Further reading 127 Key points 139
Chapter 8 Terms, questions, and discussions Key terms 139 139
Protein Folding and Self-study questions 140
Structure 129 Discussion topics 140
Primary amino acid structure is the linear sequence of amino acids joined by peptide bonds 129 Further reading Chapter 9 141
Secondary amino acid structure is a folding of the primary sequence of 129 131 Multiprotein Systems and Proteomes 143
amino acids Tertiary amino acid structures form when secondary structures come together Some cellular structural components are not directly encoded by genes 143
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Contents
Genetics of lipopolysaccharide production
The LPS has to be assembled and
translocated to the outer surface
of the cell
Peptidoglycan is built by proteins encoded
in a cluster of genes
Bacterial membrane phospholipids
are made by proteins
Extracellular polysaccharides make up
the bacterial capsule
Proteins make up bacterial cell structures
Some bacterial proteins are enzymes that
actively cause change
Bacterial secretion systems move
proteins across the bacterial membranes
The Type 1 Secretion System takes proteins
across both membranes in one step
Type 2 Secretion Systems take a protein from
the periplasm out of the cell
The Type 3 Secretion System can
inject proteins like a syringe
The Type 4 Secretion System includes
conjugation systems and DNA uptake
systems
Type 5 Secretion Systems are proteins that
secrete themselves
Type 6 Secretion Systems transport proteins
into other cells, including other bacteria
Gram-positive secretion systems
can aid protein transport across the thick
peptidoglycan layer
Efflux pump systems transport harmful
substances out of the bacterial cell
All of the expressed proteins are the
proteome
Mass spectrometry technology enables
the study of proteomes
Proteomics aids in identification of the
core genome
Mass spectrometry is being used
diagnostically to identify bacteria
Proteomics can be used to investigate
antibiotic resistance
Key points
Terms, questions, and discussions
Key terms
Self-study questions 159
Discussion topics 159
Further reading 159
Part IV Genetics, Genomics,
and Bioinformatics
Chapter 10
Genetics 163
Terms and conventions in the field
of bacterial genetics are straightforward 163
Humans have understood about
traits and inheritance long before
the term genetics 164
DNA was ignored and believed to
be too simple to be the genetic
material of inheritance 164
Bacterial genetics was the key to
demonstrating the importance of DNA 165
Insights following the recognition
of DNA as the genetic material led
us to where we are today 165
Bacterial genetics is the cornerstone
of ail genetics 166
The identification and isolation of
restriction enzymes is important for
genetics research 166
There are four types of restriction
enzymes, with type 2 being used most
in laboratories 167
The genetics of bacteria was
unraveled using conjugation 168
Physical maps can be made for any
bacterial species using restriction enzymes 169
Experimentation reveals whether a CDS is a
gene and what its function may be 170
Library generation and library screening
can identify genes and their functions 170
Random mutagenesis identifies genes
that have non-essential functions 171
The functions of genes can be determined
using knockout technologies 171
Knockout a gene and complement it back to
check the phenotype is caused by the
knocked out gene 172
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Bacterial research has helped shape the
field of genetics
Key points
Terms, questions, and discussions
Key terms
Self-study questions
Discussion topics
Further reading
Chapter 11
Genomics
Automation of Sanger sequencing
launched the era of bacterial
genome sequencing
The first genome sequence of a
free-living organism was bacterial
Early genome sequencing of bacteria
provided opportunities for new
insight and innovation
Bacterial genome sequencing
required and fueled innovation
The emergence of next-generation
sequencing technologies greatly
increased sequence data
Next-generation sequencing has limitations
Bacterial genome-sequencing
projects shift focus due to next-generation
sequencing limitations
Next-generation sequencing enables a
massive expansion of comparative genomics
Next-generation sequencing and
epidemiology
Bacterial genome-sequencing identification
of the source of outbreaks
Quick, easy sequencing means bacterial
genomes can be given a second look
Bacterial genome sequencing can uncover
bacteria never before studied
Single-molecule sequencing is more
sensitive and produces longer read lengths
Two single-molecule sequencing
technologies have emerged, including
physical reading of the DNA
Key points 186
Terms, questions, and discussions 187
Key terms 187
Self-study questions 187
Discussion topics 188
Further reading 188
Chapter 12
Bioinformatics 189
A lot can be learned from looking at strings
of A's, T's, G's, and C's 189
Bioinformatics is essential for interpreting
sequence data 189
Annotation predicts features in sequence
data and notes their locations 191
The process of creating an annotation
starts with the DNA sequence data 192
Multiple lines of investigation into
the sequence data features support
the annotation 193
Annotations tend to start with
potential genes 193
Homology and conserved protein
domains can help identify the
potential function of a CDS 194
Automated annotations rapidly produce
an annotation that needs manual curation 195
Some features in sequence data and
annotation data can confuse new
annotations 195
Naming genes is not straightforward,
with some genes having more than
one name 196
Annotation errors, including spelling
mistakes, can spread from one annotation
to many others 196
Gene locus identifiers are handy
for labeling features in annotations,
but reveal nothing about function 196
There are three major public
databases for sequence data 197
Comparative genomics finds that
there are commonly shared genes
and unique genes 197
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Comparative genomics can be done
without assembly or annotation of
sequencing data 199
Horizontally transferred gene sequences
tend to carry a signature that can identify
them 200
Genome sequence analysis can find
unexpected features in the sequence data 201
Comparative genomics on closely
related strains can reveal
biologically important information 201
Comparative genomics between
non-related species gives insight into
bacterial evolution 20B
Strain identification using sequencing
data is a powerful tool for tracking
bacterial transmission 203
Function predictions can be made
based on sequence similarity 204
Key points 206
Terms, questions, and discussions 206
Key terms 206
Self-study questions 206
Discussion topics 207
Further reading 207
PartV Bacterial Response,
Adaptation, and Evolution
Chapter 13
Bacterial Response 211
Studying responses often happens in pure
bacterial cultures 212
Two-component regulatory systems enable
bacteria to respond to their environment 212
Bacteria decrease host glucose levels
to impair the host immune response 213
Bacteria modulate the immune response
using the Type 3 Secretion System 213
Some bacteria cheat and let others
do all the work with their Type 3 Secretion
Systems 214
A response might only be appropriate
when the population is large 215
Quorum sensing makes a beautiful
bioluminescent glow in the ocean
and in the lab 216
Quorum sensing is a process to
tally the bacterial cells 216
Biofilms mature due to quorum
sensing signals 217
Quorum sensing has cheaters 218
Going from free living to biofilm involves
changes in gene expression 218
Biofilm dispersal is regulated by
different elements between different
bacterial species 219
c-di-GMP plays a key role in biofilm
regulation in P aeruginosa 220
Bacteria have their own immune system
to protect them from bacteriophages 221
Key points 222
Terms, questions, and discussions 223
Key terms 223
Self-study questions 223
Discussion topics 224
Further reading 224
Chapter 14
Bacterial Adaptation 227
Within a niche, bacteria have to adapt to
their peers and other bacteria 227
GIcNAc has a role as a signaling molecule
as well as being part of the bacterial
cell wall 228
Competitor bacteria can be killed with
specialized Type 6 Secretion Systems 228
Caulobacter differentiate between motile
and sessile cells 229
Staphylococcus aureus secrete several
proteins to inhibit host defenses as part of
adapting their niche to their needs 230
Intracellular bacteria adapt to life inside
the cells of the host 231
Mycobacterium tuberculosis adapts
both itself and its host 232
Legionella adapt by knowing when
not to grow 232
Contents xv
Group A Streptococci within the host
experience adaptation, mutation, and death 233
Adaptation of the host to enhance spread
of the infection 234
Listeria monocytogenes can adapt
to an intracellular or soil niche 234
Environmental bacteria like Lactobacillus
plantarum can live in a wide variety of niches 234
Pseudomonas aeruginosa adapts to
live in a wide variety of environments 235
Mastitis-causing bacteria Streptococcus uberis
can adapt to different niches within cows 235
Bacteria adapt to avoid recognition by the
host immune system through antigenic
variation 236
Several different species use gene conversion
as a mechanism of antigenic variation 236
Phase variation is an important means of
adaptation, but is not a means of response 237
Small noncoding RNAs also have
a role in enabling bacteria to adapt 238
Key points 238
Terms, questions, and discussions 239
Key terms 239
Self-study questions 239
Discussion topics 239
Further reading 240
Chapter 15
Bacterial Evolution 241
Evolution can be studied within bacterial
cultures 241
Bacteria can evolve within the
host and we can see this happen with
sequencing technologies 242
Antibiotic resistance is an easily observable
evolutionary event 244
Mutations can be introduced into bacterial
DNA by a variety of factors 244
Yersinia pestis, causing plague, has evolved
from Yersinia pseudotuberculosis 245
Neisseria meningitidis, causing
meningococcal meningitis and septicemia,
acquired its capsule fairly recently 246
The number of pseudogenes in a
species can reveal how recently it has
adapted to a new niche 247
Evolution of the bacterial surface to cope
with the immune system and vaccines 247
Horizontal gene transfer can bring new
genes into a species, contributing to its
evolution 248
The particular nature of an environmental
niche can create opportunities for evolution 249
It is possible for completely new genes to
evolve 249
Key points 250
Terms, questions, and discussions 250
Key terms 250
Self-study questions 251
Discussion topics 251
Further reading 251
Part VI Gene Analysis, Genome
Analysis, and Laboratory
Techniques
Chapter 16
Gene Analysis Techniques 255
Sequence searches are done to find
out what else is similar to this gene 255
Before there was BLAST, there was FASTA 255
BLAST quickly finds the most similar
sequences 256
There are five basic versions of BLAST,
addressing different search tasks 258
There are other versions of BLAST
that do specialist searches 259
Searches can look for more than
just similarities 260
Alignments of similar sequences are useful
for further analysis 261
Local alignments to compare the portions
of the sequence that are similar 261
Global alignments will align any sequences,
similar or not 262
More complex comparisons need
multiple sequence alignment algorithms 263
XVI
Contents
Protein localization can be predicted from
the amino acids 265
DNA sequence to gene to amino acid
sequence to 3D protein structure, ideally 267
De novo protein structure predictions base
structures just on the amino acids 267
Transmembrane helix prediction can find
membrane proteins 267
Homology modeling of proteins
bases structures on known structures 267
Protein threading can suggest a
protein structure based on
protein fold similarity 268
Some gene tools are used to help
design laboratory experiments 268
Key points 270
Terms, questions, and discussions 270
Key terms 270
Self-study questions 270
Discussion topics 271
Further reading 272
Chapter 17
Genome Analysis
Techniques 273
A few things happen to the genome
sequencing data before the search
for genes 273
Identification of features in genomic data
is a key aspect of analysis 274
Automated annotation pipelines usefully
combine feature identification tools 275
Visualization of an automatically generated
annotation can aid manual curation 277
Comparisons show orthologues and
paralogues, revealing evolutionary
relationships between genes 279
Genomes can be aligned, just like
genes can be aligned 279
Mauve genome alignments make stunning
figures, as well as being a useful research
tool 280
There is value in typing data, even
in the genomics age 283
Galaxy provides a full analysis
suite for biological data 284
Key points 286
Terms, questions, and discussions 286
Key terms 286
Self-study questions 286
Discussion topics 287
Further reading 287
Chapter 18
Laboratory Techniques 289
The study of bacterial genetics and genomics
fundamentally focuses on DNA, therefore
starting with lysis of bacterial cells for DNA
extraction 289
DNA extraction using phenol produces very
pure, large quantities of DNA 290
Phase separation and DNA precipitation
in a phenol DNA extraction result in
isolated DNA 290
Additional considerations for phenol
DNA extraction can improve the outcome 292
Most DNA extractions use columns 292
Troubleshooting DNA extractions
can increase yield and quality of
the DNA 293
A quick (and dirty) DNA extraction
can be achieved by boiling 294
The first recombinant DNA
experiments in the 1970s were made
possible because of restriction
enzymes, which are still used today 294
Set up a restriction digestion with
the optimal reaction conditions 295
There are a few additional considerations to
remember when doing restriction digestions 296
Restriction digestions are used to change
DNA sequences and join sequences together 296
Cut ends of DNA need to be ligated
together to complete cloning 297
Important considerations when performing
ligations 298
Cloning of sequences is often
important in bacterial genetics and
genomics research 298
Contents xvii
TA cloning exploits a feature of PCR to
rapidly clone sequences
Some commercially available kits augment
ligation and cloning with accessory proteins
and exploitation of other systems
Antibiotic resistance markers on plasmids
help us find the transformed bacterial
colonies
Blue-white screening helps us find the
colonies transformed with plasmids with
the insert
Laboratory techniques of molecular
biology are able to copy segments of DNA
in processes similar to replication
PCR can be altered slightly to address
experimental needs
Site-directed mutagenesis systems help
researchers make specific changes to DNA
Loop-mediated isothermal
amplification (LAMP) quickly amplifies
DNA at a single temperature
Following in vitro manipulation of DNA,
it has to be transformed into a bacterial cell
Calcium chloride provides a quick method to
obtain competent cells for immediate use
Chemically competent cells with Inoue
buffer have the best reputation for good
rates of transformation and reliability
Chemically competent cells can be made
with TSS buffer
Transformations using chemically
competent cells use similar methods,
regardless of how the cells were made
Electroporation provides an alternative
to chemically competent cells
The process of electroporation is sensitive to
salts, but quick to perform
Expression studies rely on extraction of
high-quality RNA, which means controlling
RNases
RNA extraction columns work similarly
to DNA extraction columns, with some
slight variations
Acidic phenol extraction of RNA makes
high-quality, pure RNA
Key points
300 Terms, questions, and discussions 315
Key terms 315
Self-study questions 315
300 Discussion topics 316
Further reading 317
302 Part VII Applications of Bacterial Genetics and Genomics
302 Chapter 19
303 Biotechnology 321
Biotechnology is far older than genetic
304 engineering Biotechnology impacts many aspects of 321
305 our lives and of research 322
Large quantities of bacteria are grown in bioreactors to yield large quantities of
307 recombinant proteins Human insulin expressed in Escherichia 322
307 coli is a classic example of biotechnology Many recombinant drugs have been made 323
309 since insulin 324
Recombinant production of influenza virus vaccines 324
309 Live recombinant vaccines use live bacteria to deliver antigens 325
310 Bioremediation uses the microbial world to correct the pollutants we have introduced into the natural world 325
311 Bioremediation using bacteria present in the environment can help us reclaim sites 326
312 Genetic modification for bioremediation can provide
312 organisms with new features 327
Bacteria can be a renewable source of bioenergy 327
312 Key points 328
Terms, questions, and discussions 329
313 Key terms 329
Self-study questions 329
313 Discussion topics 330
315 Further reading 330
Contents
xviii
Chapter 20
Infectious Diseases
331
The study of bacterial pathogen
genes has led to new drugs to
control infectious diseases
Genomics can aid in the search
for new antibiotics
Some old drugs are getting a new lease
of life due to greater depth of
understanding
Bacterial genomics has led to the
development of new vaccines
Reverse vaccinology is providing
leads for several bacterial diseases
New drugs are being developed
that will contain the virulence of bacteria
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335
Monoclonal antibody therapy is useful for a
variety of human diseases, including
infectious diseases 336
Sequencing changes our understanding of
the virulence factors that are important 337
Gene sequencing and genome
sequencing improves the resolution of
epidemiology of bacterial infectious diseases 337
Genome sequencing can improve infection
control for surgical site infections
Horizontal gene transfer between
pathogens revealed by sequencing shows
worrying trends in evolution
Genome sequencing is improving our
understanding of infections that
could impact transplant recovery
Putting discoveries into practice
Key points
Terms, questions, and discussions
Key terms
Self-study questions
Discussion topics
Further reading
338
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Chapter 21
Bacteriophages
Bacteriophages have been studied
for just over 100 years
Bacteriophages cannot replicate without
bacterial cells 344
Some bacteriophages enter latency
for a period before replication 345
The NIS2 bacteriophage has a very
small genome and was the first
genome sequenced 346
Important discoveries about genetics have
been made by studying bacteriophage X 347
TheT4 bacteriophage has a characteristic
morphology 348
The ipXl 74 bacteriophage was the
first DNA genome sequenced 349
Transduction is an important
source of horizontal gene
transfer for bacteria 349
Bacteriophages also contribute to
bacterial evolution through chromosomal
rearrangements 350
Bacteriophage and prophage genome
evolution can provide interesting insights 350
Bacteria have evolved strategies to avoid
bacteriophage infection 351
Even if bacteria become infected by
bacteriophage nucleic acids, they
can still fight back 351
Bacteriophage resistance that fights
back and uses the bacteriophages
for its own ends 352
Bacteriophage therapy is a potential
alternative treatment for
antimicrobial resistant bacteria 353
Key points 354
Terms, questions, and discussions 354
Key terms 354
Self-study questions 355
Discussion topics 355
Further reading 355
Glossary 357
Glossary of Bacterial Species 371 |
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| index_date | 2024-07-03T15:14:35Z |
| indexdate | 2024-07-10T08:56:01Z |
| institution | BVB |
| isbn | 9780815345695 9780367263768 |
| language | English |
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| spelling | Snyder, Lori A. S. Verfasser (DE-588)1213844770 aut Bacterial genetics and genomics Lori. A. S. Snyder Bosa Raton CRC Press [2020] xxiv, 389 Seiten Illustrationen, Diagramme txt rdacontent n rdamedia nc rdacarrier HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=032275734&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Snyder, Lori A. S. Bacterial genetics and genomics |
| title | Bacterial genetics and genomics |
| title_auth | Bacterial genetics and genomics |
| title_exact_search | Bacterial genetics and genomics |
| title_exact_search_txtP | Bacterial genetics and genomics |
| title_full | Bacterial genetics and genomics Lori. A. S. Snyder |
| title_fullStr | Bacterial genetics and genomics Lori. A. S. Snyder |
| title_full_unstemmed | Bacterial genetics and genomics Lori. A. S. Snyder |
| title_short | Bacterial genetics and genomics |
| title_sort | bacterial genetics and genomics |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=032275734&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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