diff --git a/gradle/libs.versions.toml b/gradle/libs.versions.toml
index c2ef3b303..278a5debf 100644
--- a/gradle/libs.versions.toml
+++ b/gradle/libs.versions.toml
@@ -15,7 +15,7 @@ nmcp = "1.6.0"
 picocli = "4.7.7"
 postgresql = "42.7.11"
 protobuf-plugin = "0.10.0"
-protobuf = "3.25.9"
+protobuf = "4.35.1"
 scala-2-12 = "2.12.20"
 scala-2-13 = "2.13.18"
 scalatest-2-12 = "3.2.20"
diff --git a/isthmus-cli/src/main/java/io/substrait/isthmus/cli/RegisterAtRuntime.java b/isthmus-cli/src/main/java/io/substrait/isthmus/cli/RegisterAtRuntime.java
index 61ab02252..084344274 100644
--- a/isthmus-cli/src/main/java/io/substrait/isthmus/cli/RegisterAtRuntime.java
+++ b/isthmus-cli/src/main/java/io/substrait/isthmus/cli/RegisterAtRuntime.java
@@ -1,8 +1,7 @@
 package io.substrait.isthmus.cli;
 
 import com.google.protobuf.Empty;
-import com.google.protobuf.GeneratedMessageV3;
-import com.google.protobuf.MessageLite;
+import com.google.protobuf.GeneratedMessage;
 import com.google.protobuf.ProtocolMessageEnum;
 import io.github.classgraph.ClassGraph;
 import io.github.classgraph.ClassInfoList;
@@ -61,8 +60,8 @@ public void beforeAnalysis(BeforeAnalysisAccess access) {
 
       try (PackageScanner substrait = new PackageScanner("io.substrait")) {
         // protobuf items
-        substrait.registerByParent(GeneratedMessageV3.class);
-        substrait.registerByParent(MessageLite.Builder.class);
+        substrait.registerByParent(GeneratedMessage.class);
+        substrait.registerByParent(GeneratedMessage.Builder.class);
         substrait.registerByParent(ProtocolMessageEnum.class);
 
         // Substrait immutables.