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Probiotics > Module 4 > Flashcards

Module 4 Flashcards

1
Q

Genomics

A

Analysis of all the genetic material in organism including genes, regulatory regions, interactions, functions, expression

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2
Q

Genome

A

Includes all Chromosomes and plasmids that constitutes and organisms DNA

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3
Q

Short protein coding regions

A

Microbial genomes

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4
Q

Smaller genomes

A

Restricted ecological niches

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5
Q

Small genomes

A

Carsonellaruddii, 160kba

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6
Q

Large genome

A

Sorongiumcellulosome, 13Mb

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7
Q

First genome and genome sequenced

A

Bacteriophage MS2 (1972 and 1976) - RNA genome

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8
Q

First sequenced DNA genome

A

Bacteriophage X174 (1977)

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9
Q

First sequenced bacterial genome

A

H. influenzae (1995)

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10
Q

Genome Steps

A

Strain –> Strategy –> Chemistry –> Assembly –> Closure and finishing –> data release –> annotation –> publish

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11
Q

Genome Annotation

A

Find ORFs and ORF function (BLASTX) and other features

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12
Q

Domain Comparisons

A

Pfam/Prosite

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13
Q

Functional Genomics

A

Ascribing gene function across a genome

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14
Q

Size involved in

A

Adaptation

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15
Q

Adaptive Capabilities

A

Biosynthetic, Stress resistance, Structure, Regulation (sensing and responding)

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16
Q

Mycoplamsa genitalium

A

Smallest self replicating genome

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17
Q

Borrelia burgdorferi

A

Small genome with few cellular biosynthetic pathways

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18
Q

Bigger Genomes

A

LABs, H. influenzae, H. pylori, C. jejuni

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19
Q

Limited Environment

A

Bigger Genomes

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20
Q

Biggest Genomes

A

Commensals

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21
Q

Bigger Genomes

A

E. coli, B. subtilis, P, aeruginosa, Y. pestis, Clostridium, MbT, S. coelicolor

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22
Q

Secondary metabolites

A

Big Genomes –> antibiotics

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23
Q

Secondary Metabolites for antibiotics

A

Streptomyces coelicolor

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24
Q

Linear Chromosomes

A

Bb , S. coelicolor

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25
Q

Multiple chromosomes

A

V. cholerae

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26
Q

Lots of plasmids

A

Bb (17 total and 50% genome)

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27
Q

Plasmids show

A

Replication, decaying genes/mutations, antigenic variation

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28
Q

Has no transposons, IS elements, phages

A

Campylobacter

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29
Q

Important for organization

A

Repeats

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30
Q

Replication

A

OriC (dnaA) and terC

31
Q

dnaA

A

Replication initiation protein

32
Q

Why Mtb vs Bs growth

A

Strand bias is 55 and 75%

33
Q

Gene Content

A

Annotation, Paralogues, Orthologoues

34
Q

Annotation

A

Sequence similarity + domain matches

35
Q

Sequence similarity

A

Gene families, regulators, transporters, biosynthesis

36
Q

Paralogue

A

Same family (homologs) in same genome with different function likely

37
Q

Orthologue

A

Homologoues (same familty) in different genomes that might have identical funtions

38
Q

Most genome sizes

39
Q

Conserved hypothetical

A

ORFans in many genomes

40
Q

Hypothetical genes

A

Unique to one genome

41
Q

Core regions

A

Shared by close relatives

42
Q

From mobile genetic elements, plasmid integration, and phages

A

Flexible regions (genomic islands)

43
Q

Gain of GI

A

Gene loss (obligate IC pathogens)

44
Q

Correlates with microbial lifestyle

A

Genome organization and content

45
Q

First genome LAB sequenced

A

1999 L. lactis –> 2003 L. plantarum

46
Q

First sequenced megaplasmid

A

L. salivarious

47
Q

General LAB features

A

Protein coding gene varies (1700 to 2000), Genome reduction, all have transposons, Many essential growth plasmids

48
Q

Clusters of Orthologous Genes of Lactobacillales (LaCOGs)

A

Genes that cluster as orthologs

49
Q

Orthologs

A

Genes from same ancestor

50
Q

LaCOGs numbers

A

86% genome, 11% LAB specific, 18% conserved among 12 genomes

51
Q

Conserved Core regions

A

The 18% LaCOGs with biochemical activity, uncharacterised genes, markers

52
Q

LysM and LaCOG012

A

Markers of Lactobacillales

53
Q

Bacilli to Lactose ancestor

A

Changes related to transition to nutritionally rich environments

54
Q

Gene loss reflects

A

Similar environmental Pressures

55
Q

Oenoe, Leume, Pedpe, Strth

A

Genome Losers

56
Q

Presence/absence patterns of key enzymes in lactate fermentation

A

Poor correlation to phenotype observed

57
Q

Types of transporters

A

Channel (VIC), 2 carrier (MF), 1 carrier (ABC), Group translocation (PTS)

58
Q

PTS

A

Membrane proteins transfer sugar to phosphatase

59
Q

Dominant transport types in LAB

A

2 carriers (9) and 1 carriers (2)

60
Q

Bidirectional Transporters

A

Nonspecfic or low (5%)

61
Q

Uptake transporters

A

aa&raquo_space; sugars > cations/anions > peptides (55%)

62
Q

Efflux Transporters

A

Drugs&raquo_space;> peptides > macromolecules (40%)

63
Q

More of these genes in LAB

A

Carbons sources and macromolecules

64
Q

Anions > Drugs

65
Q

0 Sugar transporters

66
Q

Most transporters (MFS)

A

Efflux of drugs

67
Q

Efflux

A

Drugs then lipids then peptides but excepetions

68
Q

Most Uptake

A

amino acids then sugars then inorganic cations but exceptions

69
Q

Most LABs use

70
Q

All genes that can potentially be in a species

A

Pan or supragenome

71
Q

Conserved set of genes in every member of that species

A

Core genome

72
Q

Core genes

A

Identity genes essential for life

73
Q

Dispensable genes

A

Not essential for survival

74
Q

Unknowns of genomes

A

20% or core and 45% of Pan

Probiotics (16 decks)

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