naturebiotechnologyVOLUME36NUMBER10OCTOBER20181005resourceTranslationisoneofthemostconservedandenergy-intensiveproc-essesinanycell.Inbacteria,synthesisandmaintenanceofribosomesandrelatedtranslationalmachineryaccountsformorethan40%ofthecellularenergybudget1.Thismeansthat,foranytranslatedsequence,thedeterminantsoftranslationalefficiencyarelikelytobeunderselectiontominimizecost2.Asidefromspecificregulatorymechanisms,optimizationoftranslationisthoughttoinvolvefine-tuningintrinsicsequenceproperties.Althoughhundredsofstudieshavelinkedsuchfeaturestoproteinproduction,veryfewhavealsomeasuredphysiologicaloutcomesofsequencevariationorattemptedtointegratetranslationefficienciesandphysiology3–5.Highlyexpressedgenesareenrichedincodonscognatetoabun-danttRNAs6,andgeneexpressionlevelsusuallycorrelatewithindicesdescribingtheseenrichments7,8.Biasedcodonusageisthoughttoopti-mizeelongationbypreventingwastefulribosomecollisionsandstack-ing9.Similarly,incorporationofspecificaminoacids10andsecondarystructuresintranscripts11,12hasbeenlinkedwithtranslationspeed.ExperimentalstudiesonendogenousanddesignedtranscriptshaveidentifiedtheimportanceofRNAstructuresinhinderinginitiationbyblockingribosomebindingsites13–16.Thesequenceofthe5′untranslatedregionandthefirst30–50codonsofageneisthoughttocontainmostdeterminantsoftranslationefficiency17.Selectionforatranslationspeedrampencodedatthe5′endofcodingsequencesviatheabovemecha-nismshasbeenproposedtobalancetheflowofinitiatingribosomeswiththeelongationcapacityofthedownstreamsequence18,19.Inpractice,discerningtherelativeimportanceofsequence-intrinsicfeaturesandtheinteractionsamongthemhasprovendifficult.Thisisbecausemostsequence–activitystudiesinvolveanalysisofendog-enousgenes,whichhaveevolvedhighlyscrambledcontrolsignals.Forexample,abiasforN-terminalpositivechargeisfoundalmostexclu-sivelyinweaklyexpressedmembraneproteins.Thistypeofproteinsequenceenablesassociationwiththecytosolicmembraneleaflet20ratherthanribosomalslowing19,butitisassociatedwithbo...
