Re-annotating the Mycoplasma pneumoniae genome sequence:: adding value, function and reading frames

Autoren

T Dandekar

DOI

10.1093/nar/28.17.3278

eISSN

1362-4962

Ausgabe der Veröffentlichung

17

Zeitschrift

Nucleic Acids Research

Paginierung

3278 - 3288

Datum der Veröffentlichung

2000

Status

Published

Herausgeber

Oxford University Press (OUP)

Herausgeber URL

http://dx.doi.org/10.1093/nar/28.17.3278

Datum der Datenerfassung

2017

Titel

Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames

Ausgabe der Zeitschrift

28

Data source: Crossref

Abstract

Four years after the original sequence submission, we have re-annotated the genome of Mycoplasma pneumoniae to incorporate novel data. The total number of ORFss has been increased from 677 to 688 (10 new proteins were predicted in intergenic regions, two further were newly identified by mass spectrometry and one protein ORF was dismissed) and the number of RNAs from 39 to 42 genes. For 19 of the now 35 tRNAs and for six other functional RNAs the exact genome positions were re-annotated and two new tRNA(Leu) and a small 200 nt RNA were identified. Sixteen protein reading frames were extended and eight shortened. For each ORF a consistent annotation vocabulary has been introduced. Annotation reasoning, annotation categories and comparisons to other published data on M.pneumoniae functional assignments are given. Experimental evidence includes 2-dimensional gel electrophoresis in combination with mass spectrometry as well as gene expression data from this study. Compared to the original annotation, we increased the number of proteins with predicted functional features from 349 to 458. The increase includes 36 new predictions and 73 protein assignments confirmed by the published literature. Furthermore, there are 23 reductions and 30 additions with respect to the previous annotation. mRNA expression data support transcription of 184 of the functionally unassigned reading frames.

Addresses

EMBL, Postfach 102209, D-69012 Heidelberg, Germany, Max Delbrück Centre for Molecular Medicine, Robert-Rössle-Strabetae 10, 13092 Berlin-Buch, Germany.

Autoren

T Dandekar
M Huynen
JT Regula
B Ueberle
CU Zimmermann
MA Andrade
T Doerks
L Sánchez-Pulido
B Snel
M Suyama
YP Yuan
R Herrmann
P Bork

DOI

10.1093/nar/28.17.3278

eISSN

1362-4962

Externe Identifier

PubMed Identifier: 10954595
PubMed Central ID: PMC110705

Open access

false

ISSN

0305-1048

Ausgabe der Veröffentlichung

17

Zeitschrift

Nucleic acids research

Schlüsselwörter

Mycoplasma pneumoniae
Bacterial Proteins
RNA, Bacterial
RNA, Messenger
Oligonucleotide Array Sequence Analysis
Sequence Alignment
Computational Biology
Phylogeny
Amino Acid Sequence
Genes, Bacterial
Genome, Bacterial
Open Reading Frames
Molecular Sequence Data
Mass Spectrometry

Sprache

eng

Medium

Print

Paginierung

3278 - 3288

Datum der Veröffentlichung

2000

Status

Published

Datum der Datenerfassung

2000

Titel

Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames.

Sub types

Research Support, Non-U.S. Gov't
research-article
Journal Article

Ausgabe der Zeitschrift

28

Files

https://europepmc.org/articles/PMC110705?pdf=render

Data source: Europe PubMed Central

Abstract

Four years after the original sequence submission, we have re-annotated the genome of Mycoplasma pneumoniae to incorporate novel data. The total number of ORFss has been increased from 677 to 688 (10 new proteins were predicted in intergenic regions, two further were newly identified by mass spectrometry and one protein ORF was dismissed) and the number of RNAs from 39 to 42 genes. For 19 of the now 35 tRNAs and for six other functional RNAs the exact genome positions were re-annotated and two new tRNA(Leu) and a small 200 nt RNA were identified. Sixteen protein reading frames were extended and eight shortened. For each ORF a consistent annotation vocabulary has been introduced. Annotation reasoning, annotation categories and comparisons to other published data on M.pneumoniae functional assignments are given. Experimental evidence includes 2-dimensional gel electrophoresis in combination with mass spectrometry as well as gene expression data from this study. Compared to the original annotation, we increased the number of proteins with predicted functional features from 349 to 458. The increase includes 36 new predictions and 73 protein assignments confirmed by the published literature. Furthermore, there are 23 reductions and 30 additions with respect to the previous annotation. mRNA expression data support transcription of 184 of the functionally unassigned reading frames.

Autoren

T Dandekar
M Huynen
JT Regula
B Ueberle
CU Zimmermann
MA Andrade
T Doerks
L Sánchez-Pulido
B Snel
M Suyama
YP Yuan
R Herrmann
P Bork

Autoren-URL

https://www.ncbi.nlm.nih.gov/pubmed/10954595

DOI

10.1093/nar/28.17.3278

eISSN

1362-4962

Externe Identifier

PubMed Central ID: PMC110705

Ausgabe der Veröffentlichung

17

Zeitschrift

Nucleic Acids Res

Schlüsselwörter

Amino Acid Sequence
Bacterial Proteins
Computational Biology
Genes, Bacterial
Genome, Bacterial
Mass Spectrometry
Molecular Sequence Data
Mycoplasma pneumoniae
Oligonucleotide Array Sequence Analysis
Open Reading Frames
Phylogeny
RNA, Bacterial
RNA, Messenger
Sequence Alignment

Sprache

eng

Country

England

Paginierung

3278 - 3288

Datum der Veröffentlichung

2000

Status

Published

Datum, an dem der Datensatz öffentlich gemacht wurde

2000

Titel

Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames.

Sub types

Journal Article
Research Support, Non-U.S. Gov't

Ausgabe der Zeitschrift

28

Data source: PubMed

Re-annotating the Mycoplasma pneumoniae genome sequence:: adding value, function and reading frames

Files

Tools