While annotating my transcripts, I understand how little I know about molecular biology in plants. As everything was studied in Arabidopsis (note that I do not mean everything in Arabidopsis is studied…), the best way to meet a gene is still understanding what it does in Arabidopsis.
Usually what I do is search the name of the gene (spell out the whole thing instead of using acronyms because the latter is not very intuitive and sometimes cause confusions.). Usually several literature where the gene is described will pop up.
If you’re lucky enough or the gene you searched for is important enough, you will hit papers that are dedicated to that gene or gene family. Even better, the results of the paper (usually the function of the gene or gene families) will be in the title!
If not, abstracts would be enough. If all the hits that returned are studies INVOLVED your gene, you then have to read the introduction to know better what it does (ctrl+F for your gene in the paper).
For example, I would like to know what AFB5 (Auxin F-box Protein 5) does.
- Search for Auxin F-box Protein 5
- Search for AFB5 (extra caution on whether you’re talking about the same AFB5). a. The first hit is a paper INVOLVES AFB5. Firstly check whether it is the same AFB5 that we are talking about. They are talking about “AUXIN SIGNALING F-BOX proteins “, looks OK. Usually it is a good idea to know what the family does. Here we go in the abstract:
Auxin acts by binding the F-box protein transport inhibitor response 1 (TIR1) and promotes the degradation of the AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) transcriptional repressors.
Later in the introduction:
Auxin-dependent degradation of the Aux/IAAs occurs through the action of a SKP1–Cullin–F-box (SCF)-type E3 ligase called SCFTIR1/AFB1–5. The F-box protein TIR1 and the related proteins AFB1, AFB2, AFB3, AFB4 and AFB5 are the substrate-specificity determinants, or substrate receptors, for the SCF
aka: AFBs response to Auxin and can promote/repress the production of Auxin. (indole-3-acetic acid (IAA) is the most abundant and the basic auxin natively occurring and functioning in plants. It generates the majority of auxin effects in intact plants, and is the most potent native auxin.–wiki) Now how about AFB5? We need to be this careful. Remember those auxin response factors? They can be either activators or repressors! Nothing too horrible:
The amount of heterologous proteins in yeast was assessed by immunoblot analysis showing that TIR1, AFB1, AFB2 and AFB5 fusion proteins were expressed at similar levels.
IAA3 also bound TIR1, AFB1 and AFB2 at this concentration but was a poor substrate for AFB5
Therefore we can take AFB5 as a variation of other members.
Other databases:
- NCBI Gene: the Summary and Primary source link can be helpful.
- wikigenes gives “High impact information” on genes but not necessarily the function of genes.
- iHop: a gateway for other databases.
- Science Journals > Science Signaling Home > Database of Cell Signaling
- GenScript: not helpful at all
- TAIR: only for AT. The description can be helpful.
- Sometimes the General annotation(Comments) in UniProtKB is helpful. For example Auxin transport protein BIG:
Required for auxin efflux and polar auxin transport (PAT) influencing auxin-mediated developmental responses (e.g. cell elongation, apical dominance, lateral root production, inflorescence architecture, general growth and development). Controls the elongation of the pedicels and stem internodes through auxin action. Involved in the expression modulation of light-regulated genes. Represses CAB1 and CAB3 genes expression in etiolated seedlings. Confers sensitivity to the auxin transport inhibitors N-1-naphthylphthalamic acid (NPA), 2-carboxyphenyl-3-phenylpropane-l,2-dione (CPD), and methyl-2-chloro-9-hydroxyfluorene-9-carboxylate (CFM). Influences the polarized subcellular distribution of the auxin transporter PIN1 in response to auxin transport inhibitors. Plays a role in the regulation of responses to phytohormones such as auxin, cytokinins, ethylene and gibberellic acid (GA), particularly during light-mediated stimuli (e.g. shade ovoidance, etiolation). Required for pericycle cell activation to form lateral root primordia (LRP) in both high and low phosphate P conditions. Necessary for the plant-growth promotion and lateral root development mediated by the fungus Trichoderma virens. Ref.1 Ref.4 Ref.5 Ref.6 Ref.8 Ref.9 Ref.10 Ref.11 Ref.13
Note there are references at the end which can be very helpful.
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