Tome: Temperature optima for microorganisms and enzymes

Tome (Temperature optima for microorganisms and enzymes) is an open source suite for two fundamental applications:

• predict the optimal growth temperature from proteome sequences
• get homologue enzymes for a given ec number with/without a sequence that have a temperature optima in a specified range.

Citation

Li, G., Rabe, K. S., Nielsen, J. & Engqvist, M. K. M. Machine learning applied to predicting microorganism growth temperatures and enzyme catalytic optima. bioRxiv (2018). doi:10.1101/522342

System

• macOS
• Linux

Installation

(1). Download tome package

(2). Open your terminal

(3). Change directory to the tome package

cd [directory to tome, where setup.py is]

(4). Run following command

pip install -e .

(5) Now you can use 'tome' via command line.

There is a folder named 'test' in the package. One can use the instructions in 'Usage' section to test the package.

Depedences

• ncbi-blast-2.7.1+ (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/) (This is only mandatory for 'tome predOGT -seq')
• pandas
• Biopython
• numpy
• sklearn
• Pyhton 2.7 or Python 3

Usage:

1. Prediction of optimal growth temperature

1.1 Prediction of optimal growth temperature for one microorganism

tome predOGT --fasta test/proteomes/pyrococcus_horikoshii.fasta

Then you will get following results:

FileName	predOGT (C)
pyrococcus_horikoshii.fasta	94.0

1.2 Predict optimal growth temperatures for a list of microorganisms. Fasta files must end with .fasta

tome predOGT --indir test/proteomes/ -o test/proteomes/predicted_ogt.tsv

Then you will get an tab-seperated output file predicted_ogt.tsv with following contents:

FileName	predOGT (C)
succinivibrio_dextrinosolvens.fasta	38.27
pyrococcus_horikoshii.fasta	94.0
caldanaerobacter_subterraneus.fasta	70.0

1.3 train the model

In case there would be some warnings due to the versions of sklearn when loading the model, one can use following command to train the model again:

tome predOGT --train

Expected output after training is

A new model has beed successfully trained.
Model performance:
        RMSE: 2.159489340036136
          r2: 0.9552614628185572
  Pearson r:(0.9775886084277753, 0.0)
  Spearman r:SpearmanrResult(correlation=0.93331975456613, pvalue=0.0)

Saving the new model to replace the original one...
Done!

2. Get enzyme sequences

The first time this command is run two files totaling ~2.5 GB will be downloaded from the Zenodo data repository (https://zenodo.org/record/2539114#.XDyAUc_0l0s). These files contain the enzyme annotation data.

2.1 Get enzymes for a given ec number.

For example, we want to get the enzymes with EC 3.2.1.1 with a temperature optima higher 50 °C.

tome getEnzymes --ec 3.2.1.1 --temp_range 50,200 --data_type Topt --outdir test/enzyme_without_seq/

Two output files will be generated: test/enzyme_without_seq/3.2.1.1_all.fasta and test/enzyme_without_seq/3.2.1.1_all.tsv 3.2.1.1_all.fasta contains all sequences for this EC number. This can be used for mutisequence alignment with tools like Clustal Omega (https://www.ebi.ac.uk/Tools/msa/clustalo/) enzyme_without_seq/3.2.1.1_all.tsv contains following columns:

• uniprot id
• domain: Domain information of source organism (Archaea/Bacteria/Eukaryote)
• organism: name of source organism
• ogt: optimal growth temperature of source organism
• ogt_source: if the growth temperature is predicted or experimentally determined
• topt: temperature optima of the enzyme
• topt_source: if topt is predicted or experimentally determined
• seqeunce: protein sequence

One can also use following command to find enzymes from organisms with a OGT fall into the temperature range specified with --temp_range. The output files have the same format as above described.

tome getEnzymes --ec 3.2.1.1 --temp_range 50,200 --data_type OGT --outdir test/enzyme_without_seq/

2.2 Get homologous enzymes for an given ec number and sequence.

For example, we want to get all homologs of an enzyme with EC 3.2.1.1 from Photobacterium profundum (OGT = 13°C). We want those homologs with a temperature optima higher 50 °C. The sequence for this enzyme is

>Q1Z0D7
MTSLFNTEYASTLSAPSVATNVILHAFDWPYSKVTENAKAIADNGYKAILVSPPLKSFHSKDGTQWWQRYQPQDYRVIDN
QLGNTNDFRTMVEILSLHDIDIYADIVFNHMANESHERSDLNYPNSNIISQYKDKREYFDSIKLFGDLSQPLFSKDDFLS
AFPIKDWKDPWQVQHGRISSGGSDPGLPTLKNNENVVKKQKLYLKALKKIGVKGFRIDAAKHMTLDHIQELCDEDITDGI
HIFGEIITDGGATKEEYELFLQPYLEKTTLGAYDFPLFHTVLDVFNKNASMASLINPYSLGSALENQRAITFAITHDIPN
NDVFLDQVMSEKNEQLAYCYILGRDGGVPLIYTDLDTSGIKNSRGKPRWCEAWNDPIMAKMIHFHNIMHCQPMVIIEQTL
DLLVFSRGHSGIVAINKGKTAVCYKLPAKYSEQDHTEIKEVINMEGVKLSPPSLSTEAGVILQLPAQSCAMLMV

There should be only one sequence in the fasta file. If more than 1 sequence is provided, only the first sequence would be used.

tome getEnzymes --seq test/enzyme_with_seq/test.fasta --ec 3.2.1.1 --temp_range 50,200 --data_type Topt --outdir test/enzyme_with_seq/

Two output files will be created:

• Q1Z0D7_homologs.fasta: a fasta file which contains sequences for all homologs of query enzyme
• Q1Z0D7_homologs.tsv: a tab-seperated file with following columns:
  • uniprot id
  • domain: Domain information of source organism (Archaea/Bacteria/Eukaryote)
  • organism: name of source organism
  • ogt: optimal growth temperature of source organism
  • ogt_source: if the growth temperature is predicted or experimentally determined
  • topt: temperature optima of the enzyme
  • topt_source: if topt is predicted or experimentally determined
  • Identity(%) from blast
  • Coverage(%) from blast
  • seqeunce: protein sequence

In this test case, 44 homologs with a temperature optima higher than 50 °C were found.

One can also use following command to find homologous enzymes from organisms with a OGT fall into the temperature range specified with --temp_range. The output files have the same format as above described.

tome getEnzymes --seq test/enzyme_with_seq/test.fasta --ec 3.2.1.1 --temp_range 50,200 --data_type OGT --outdir test/enzyme_with_seq/

In this case, 13 homologs from organisms with a OGT higher than 50 °C were found

Help:

Use following commands you can get detailed information about the arguments of tome.

tome --help/-h
tome predOGT --help/-h
tome getEnzymes --help/-h

Or you can directly contact Martin Engqvist: [email protected] or Gang Li: [email protected]

Gang Li